sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fa382747032c875f6af587938615a8330eb4fb07f04ccc54e33fcfd7e7272e82 | Python | 25,020 | 351 | import argparse
##-------------------------------------------------------------------------------------------------------------------##
# Where to store the data / results / models / plots
store = "./store"
##------------------------------------------------------------------------------------------------------------... |
9330e87f35a37f21e6a47bff9add9e1ec65fdd42ec0a15dd2480a9564dc6b3d5 | Python | 25,038 | 620 | """
Object Store plugin for the Integrated Rule-Oriented Data System (iRODS)
"""
import logging
import os
import shutil
import ssl
import threading
from datetime import datetime
from pathlib import Path
try:
import irods
import irods.keywords as kw
from irods.exception import (
CollectionDoesNotEx... |
ac682bc78eb69cf2fe2b4d5fae1e370ad0a8f89cd71120b9c8eebb7756c87a9e | Python | 25,048 | 547 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
5195b4b6a8d4132c95723910b27d540fa946897a4920d87bd7b2d6edb02adf18 | Python | 25,082 | 644 | #Tools for mesh-based operations
#Smoothing,
import nibabel as nb
import numpy as np
import subprocess
import os
import potpourri3d as pp3d
from meld_classifier.paths import BASE_PATH, MELD_PARAMS_PATH
import matplotlib.pyplot as plt
# import paths as paths
def find_nearest_multi(array, value):
new_array = np.arr... |
6bb2b318d9d54038e9ed497aab607aae458d8f29345ad857631e6a6ceaedab04 | Python | 25,089 | 604 | """Bounded user-action provenance graph for Galaxy histories.
For each selected top-level history item, resolves its producing
tool_request and that tool_request's declared inputs from the
submission payload, one hop out from the seed.
"""
import json
import logging
from typing import (
Literal,
Optional,
... |
e85d49353d6930432df82dbb1f73ec759605fb9dd2ac932b1da6a443ca43ecd8 | Python | 25,098 | 662 | """
Minimum cost flow algorithms on directed connected graphs.
"""
__all__ = ["network_simplex"]
from itertools import chain, islice, repeat
from math import ceil, sqrt
import networkx as nx
from networkx.utils import not_implemented_for
class _DataEssentialsAndFunctions:
def __init__(
self, G, multigr... |
d98cb7495bba7e55b65eba24e7a973c34df8730ac470a844e709bba1fc3239bb | Python | 25,104 | 724 | import itertools
import os
import shutil
import tempfile
import unittest
from copy import copy
import numpy as np
from bsb import MPI, Scaffold, get_simulation_adapter, read_results
from bsb_test import (
ConfigFixture,
MorphologiesFixture,
NetworkFixture,
NumpyTestCase,
RandomStorageFixture,
)
fro... |
9afd2971993e510d7a96ba0bf4460ab82a065af902f114cc8fb6e67310ef4c85 | Python | 25,111 | 737 | import atexit
import os.path
import shutil
import warnings
import numpy as np
import pytest
from numpy.testing import assert_array_equal
from zarr._storage.store import DEFAULT_ZARR_VERSION
from zarr.codecs import Zlib
from zarr.core import Array
from zarr.creation import (array, create, empty, empty_like, full, full... |
8737844cf3801d0dd9aa78417167afe6aa8dba7e1a41667df910608c1620cce4 | Python | 25,166 | 646 | """
The interactive REPL driven from a web page.
:class:`WebRepl` runs what a page sends as the REPL runs what is typed
at its prompt, with the same commands and the same output: each
submission's output is rendered as it is on a terminal, by ``rich``, and
returned as HTML for the page to show. It is what the in-brows... |
f404414697a7473986f2fa5701f91c6e6ee9b9615b387abf9cac025475d85bd4 | Python | 25,179 | 804 | import argparse
import sys
from pathlib import Path
from learnMSA.run import util
from learnMSA import Configuration
class LearnMSAArgumentParser(argparse.ArgumentParser):
def error(self, message : str):
sys.stderr.write('error: %s\n' % message)
self.print_help()
sys.exit(2)
def parse_arg... |
ed4f70097cf84872b45de62bb359362a3620ad85500e7b6cda08102f3535f29d | Python | 25,181 | 803 | import random
import pytest
import networkx as nx
from networkx import convert_node_labels_to_integers as cnlti
from networkx.algorithms.simple_paths import (
_bidirectional_dijkstra,
_bidirectional_shortest_path,
)
from networkx.utils import arbitrary_element, pairwise
class TestIsSimplePath:
"""Unit t... |
3c54c81910222d41c2d1c5d982d6b6d598072f014aa3a5c7634302ecee434598 | Python | 25,184 | 779 | """Compute and plot ERPs over subjects."""
# %%
# Imports
import itertools
import json
import warnings
import matplotlib.pyplot as plt
import mne
import numpy as np
import pandas as pd
import pingouin
import scipy.stats
import seaborn as sns
import statsmodels.stats.multitest
from scipy.spatial.distance import squaref... |
388b946efeb7507f6ae82328d87e2cd4577e5746d94c8394e30b5918478a6a1e | Python | 25,214 | 624 | # -*- coding: utf-8 -*-
"""
Created on 2020.05.19
@author: Jiahua Rao, Weiming Li, Hui Yang, Jiancong Xie
Code based on:
Yang et al "Analyzing Learned Molecular Representations for Property Prediction" & "A Deep Learning Approach to Antibiotic Discovery" -> https://github.com/chemprop/chemprop
Song et al "Communicati... |
17c07644c19fc32eaa93821fee78d12ebadc60d8afabd0862150e7672c446b7b | Python | 25,221 | 698 | import matplotlib
#matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from matplotlib import gridspec
import parmap
import numpy as np
import pandas as pd
import os
import shutil
import cv2
import scipy.io as sio
import glob2
from numba import jit
from sklearn.svm import SVC # "Support ... |
c513c3868869df4bf9939e28fb92926eb1f62e261f4f57fc6f2016e13f6aea60 | Python | 25,253 | 610 | import os
import numpy as np
import pandas as pd
import scipy as sp
from src.routines import LoadFC
from src.imaging_derivs import DataVector, DataMatrix
from src.energy import matrix_normalization, expand_states, control_energy_helper, \
get_gmat, grad_descent_b, minimum_energy_fast
from src.prediction import corr... |
e86f7629a5775fd6f08a8ae03f557b5807e24292a7a44ac52914d49d4279274f | Python | 25,267 | 610 | """Compare predicted gene essentiality with Hart 2015 experimental fitness data.
Python port of code/test/evaluateHart2015Essentiality.m. Given the genes predicted
essential in each cell-line-specific model (see estimateEssentialGenes.py), this
computes TP/TN/FP/FN and the derived metrics (accuracy, sensitivity, speci... |
7d6ddfc25add57bde9d8b4ffef123705c933071d87a9d2db750338ca80ec529b | Python | 25,285 | 519 | # -*- coding: utf-8 -*-
import numpy as np
import pandas as pd
import os
import copy
import seaborn as sb
from matplotlib import pyplot as plt
from scipy.signal import argrelextrema
from scipy import stats
def smoothen(row,new_growth_data,radius,column):
#calculate smooth growth by averaging the last ... |
04bfb4f76bc2018999c47e13e7ed056ad6b34c6a4dc9fdce8118ab1ee6697c4e | Python | 25,303 | 701 | """A mixin to extend a class that has self.driver with higher-level constructs.
This should be mixed into classes with a self.driver and self.default_timeout
attribute.
"""
import abc
import threading
from contextlib import contextmanager
from typing import (
Any,
cast,
Generic,
Literal,
Optional,... |
8b24a0a176bc9cec6d4e6202af4aee29779d9773afe76c42256f83667a9fff02 | Python | 25,313 | 785 | import numpy as np
import nibabel as nib
import scipy.ndimage
from itertools import product
from nl_expr.exceptions import NeuroLangException
from .aabb_tree import AABB, Tree, aabb_from_vertices, Node
__all__ = [
'region_union', 'region_intersection', 'region_difference',
'region_set_from_masked_data', 'take... |
d2b8d49caa7c86b5a9494609b259f7e81b5ebfe2490b8e9d5725fd590bb57e55 | Python | 25,317 | 685 | """ Sources are objects that inject the fields into the grid.
Available sources:
- PointSource
- LineSource
"""
## Imports
# other
from math import pi, sin
# typing
from .typing_ import Tuple, Number, ListOrSlice, List
from numpy import ndarray
from torch import exp
# relatvie
from .grid import Grid
from .backend... |
893739047234f0b0f1d32e9f8ff03af716077a634a578b80944f02349ad8b6f8 | Python | 25,339 | 453 | import tensorflow as tf
import numpy as np
from learnMSA.legacy.TotalProbabilityCell import TotalProbabilityCell
from learnMSA.legacy.Utility import deserialize
from learnMSA.legacy.Bidirectional import Bidirectional
class MsaHmmLayer(tf.keras.layers.Layer):
""" A layer that computes the log-likelihood and poster... |
22d5dd82a9edfdf3f1d9af5c758bb2b3e3858687f8fb315eb341ac09b080e1cf | Python | 25,350 | 563 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
"""
Utilities for working with data for an Ax experiment.
Unlike the Ax Data object, "data" here refers to both the ... |
8f34c8e0271489ae00ba3b2188ac00b1887aca777da18f095ecd1241099d19b5 | Python | 25,357 | 510 | """All pain comparison as sanity check"""
import os,json,glob,sys
from os.path import join as opj
from nipype.interfaces.spm import Level1Design, EstimateModel, EstimateContrast, OneSampleTTestDesign, Threshold, TwoSampleTTestDesign
from nipype.algorithms.modelgen import SpecifySPMModel
from nipype.interfaces.utility ... |
ee393ccb94dafc74cf566cc746ffbb295940ec455b168d32096275a8963c34ac | Python | 25,376 | 766 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import os
from collections.abc import Callable, Generator, Sequence
from logging import Logger
from ty... |
1f5d5d0c9d17a317d11aade9a3b1b143dfa7a0213d46fe36ed8e771bff231366 | Python | 25,378 | 679 | """Unit tests for layout functions."""
import pytest
import networkx as nx
np = pytest.importorskip("numpy")
pytest.importorskip("scipy")
class TestLayout:
@classmethod
def setup_class(cls):
cls.Gi = nx.grid_2d_graph(5, 5)
cls.Gs = nx.Graph()
nx.add_path(cls.Gs, "abcdef")
cl... |
db7f6899b2c6a27a2384405f641fad36ae66db821a192c794df87654252838f5 | Python | 25,379 | 575 | """
Created on Jun 12, 2018.
Creates a topoplot from provided data, indicating either size of change or size of change and significance.
:author: voodoocode
"""
import numpy as np
import scipy.interpolate
import skimage.filters
import matplotlib # @UnusedImport
import matplotlib.markers
matplotlib.use("QtAgg") # ... |
288fbb6c8a85f138bb5cd45962699393d0dabe9a4c4dcc67e7d24d0f9afd69b9 | Python | 25,380 | 761 | # -*- coding: utf-8 -*-
"""
Cells
=====
Expert cell image processing pipeline.
This module provides the basic routines for processing immmediate eaerely
gene data.
The routines are used in the :mod:`ClearMap.Scripts.CellMap` pipeline.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ ... |
a409c574e7540a3849973d630af71b9faf9d8b70bf096347b8f7422fbaa516ad | Python | 25,387 | 976 | """
Unit tests for inhibitory cell density computation
(linear program minimizing distances to initial estimates)
"""
import numpy as np
import numpy.testing as npt
import pandas as pd
import pandas.testing as pdt
import pytest
import atlas_densities.densities.inhibitory_neuron_densities_optimization as tested
from a... |
027bb069c71d5fbf4f7ebe7ac97e5f9b9ef83df392eac85522eab93664a9eb08 | Python | 25,391 | 591 | ## This script runs a FreeSurfer reconstruction on a participant
## Within your MELD folder should be an input folder that contains folders
## for each participant. Within each participant folder should be a T1 folder
## that contains the T1 in nifti format ".nii" and where available a FLAIR
## folder that contains... |
382da646cf215dc95e7ed5ff59481aecced6c080d3bffd9972e7b9cc83e59075 | Python | 25,442 | 694 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
575ffed93c738c5adb6f79c3f1fc7141d2a045822094a2d6ff0b4a19c69cd52c | Python | 25,446 | 604 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from collections import OrderedDict
from collections.abc import Sequence
from logging import Logger
fr... |
26d92a556c5f612925256d4c9b00f172888c33455e0dad7a838438de69cec4a4 | Python | 25,451 | 690 | """QC metrics for detecting tile-boundary segmentation artifacts.
Cells cut by tile borders during segmentation have characteristic
straight edges that natural cell boundaries never produce. This module
computes per-cell metrics that quantify this artifact:
- **max_straight_edge_ratio**: length of the longest straig... |
f9bef6d6c484c725e2c47c655cbfac8d2e407b3aee89c71ad2a042330b99739b | Python | 25,467 | 712 | from __future__ import annotations
import argparse
import json
import os
import pickle
import socket
import time
from pathlib import Path
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.utils.data import DataLoader, Subset
from torchvision import datasets, transforms
from spikingjelly.a... |
e914e7287d54678b3d0ea985acaa1e1f0fd34fffdfea4b6675d4db39269ae01a | Python | 25,495 | 724 | import functools
import itertools
import numpy as np
from scipy.spatial.transform import Rotation
from ._util import rotation_matrix_from_vectors
from .exceptions import EmptyVoxelSetError
from .trees import BoxTree
class VoxelData(np.ndarray):
"""
Chunk identifier, consisting of chunk coordinates and size.... |
d94fef1b5a03d055a6ed071230eb14d961a0e6eb680cd4bbf8c2ff6e4f19c410 | Python | 25,527 | 649 | # io.py
# Authors: Jacob Schreiber <jmschreiber91@gmail.com>, Ivy Raine <ivy.ember.raine@gmail.com>
from collections import OrderedDict
import os
import textwrap
import h5py
import hdf5plugin
from typing import List, Literal, Union
import numpy as np
import scipy
from . import util
from . import meme_writer
from .... |
80a88194e1d386d3ce2bff36731a5b0dc3bccf0011f223ff647b0333aadd5942 | Python | 25,547 | 493 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thur August 30 2018
@author: chrisarcadia
@description: script to review a library sourceplatesheet and to optionally
generate a mass list and Echo recipe for that library
"""
# Import python libraries
import chemcpupy
import ... |
c3bdc47716123a4da0b1a0221c62f6759ac295da0f8ae46bd9e4dfa9c16f09db | Python | 25,570 | 717 | """setuptools.command.egg_info
Create a distribution's .egg-info directory and contents"""
from distutils.filelist import FileList as _FileList
from distutils.errors import DistutilsInternalError
from distutils.util import convert_path
from distutils import log
import distutils.errors
import distutils.filelist
import... |
38f6e496aa31e3a5a107593dfa5d72e83df537166113a63a64bc617ce2eb9c58 | Python | 25,576 | 694 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import unittest
from logging import Logger
from typing import Any
import numpy as np
from ax.adapter.... |
53c5ee62c6a297fa18ec20f7dc7812e0e6a74a0dd4e1ea9f97a5834fce9e658e | Python | 25,587 | 725 | import io
import time
import pytest
import networkx as nx
def test_gexf_v1_3(tmp_path):
"""'Basic graph' example from https://gexf.net/schema.html"""
# GEXF file from published example
data = """<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://gexf.net/1.3" version="1.3">
<graph mode="stat... |
10e9d9287f902502ce56c7d92cce9325a1dbe9de2c00ddd495957356f046f805 | Python | 25,608 | 568 | '''
Script to evaluate the model trained on noisy training dataset, with noisy test dataset
'''
import os
os.environ["CUDA_DEVICE_ORDER"]="PCI_BUS_ID"
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
import numpy as np
import torch
torch.set_num_threads(1)
from torch.autograd import Variable
from matplotlib import pyplot as ... |
b5ad63a780793c6056ce8015d6ce3c58bb870912024272bb17d9bf9322b867c8 | Python | 25,609 | 705 | from __future__ import absolute_import
from contextlib import contextmanager
import zlib
import io
import logging
from socket import timeout as SocketTimeout
from socket import error as SocketError
from ._collections import HTTPHeaderDict
from .exceptions import (
BodyNotHttplibCompatible, ProtocolError, DecodeErr... |
cacd1d6b09382f05aed4b1207b6c1641d4f0ade77e6474ef50f7b5203c9694d3 | Python | 25,616 | 688 | import collections
from operator import contains, eq, not_
from typing import AbstractSet, Callable, Tuple
from nl_expr.exceptions import (
CouldNotTranslateConjunctionException,
ForbiddenExpressionError,
NegativeFormulaNotNamedRelationException,
NegativeFormulaNotSafeRangeException,
)
from nl_expr.exp... |
d6b04f8ee6cf3f11b3a7b8e7fa4f852f1104b305c7b18f89752ccbfda3498001 | Python | 25,637 | 469 | from oct import *
#from oct.post import Post
import numpy as np
import napari
from magicgui import magicgui
from qtpy.QtCore import Qt
from qtpy.QtWidgets import QSlider,QFileDialog,QLineEdit
import enum
from napari.layers import Image
# Enums are a convenient way to get a dropdown menu
class Operation(enum.Enum):
... |
02de54b546d83bee93569b721c32798c7e5c81d7acae75fc9d6d4359b2a08883 | Python | 25,694 | 535 | import numpy as np
import math
import torch
from torch import nn
from torch.nn import functional as F
from models.fc.layers import fc_layer,fc_layer_split
from models.fc.nets import MLP
from models.conv.nets import ConvLayers,DeconvLayers
from models.cl.continual_learner import ContinualLearner
from models.utils import... |
d705bd0e12aa77c12313111a37936209d63b9fd5fc799cc4636acf6ebee9bd40 | Python | 25,726 | 597 | import random
import torch
import os
import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from torch.utils.data import RandomSampler, BatchSampler
from .utils import calculate_accuracy, Cutout, calculate_accuracy_by_labels, calculate_FP, calculate_FP_Max
from .newtrainer import Trainer... |
f629bfe19d66a33eacf2bdb6a941b9f40572aa0d7ddefb3df4873b472a5a4d34 | Python | 25,727 | 503 | """
`bsb-core` is the backbone package contain the essential code of the BSB: A component
framework for multiscale bottom-up neural modelling.
`bsb-core` needs to be installed alongside a bundle of desired bsb plugins, some of
which are essential for `bsb-core` to function. First time users are recommended to
install ... |
a4c434efd9e56f5bc5b9b53d3df14181709ff3a29edc5ba3d8adc58a05caa2c5 | Python | 25,729 | 678 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# ex: set sts=4 ts=4 sw=4 et:
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See the COPYING file distributed along with the smile package for the
# copyright and license terms.
#
# ## ### ### ### ### ### ... |
118e18efe4ff2cf0fd82302adf9533f2f72a1a1aa39ae58e6a9b351b17791a2e | Python | 25,761 | 515 | # -*- coding: utf-8 -*-
import pandas as pd
import os
import copy
import numpy as np
import time
import re
from skimage import io
from scipy import ndimage
from scipy.ndimage import morphology
from matplotlib import pyplot as plt
input_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
... |
b3c47390992718baa12e10c63f9b1ac56db15731c972778f3510a9776d638cde | Python | 25,771 | 642 | from __future__ import print_function
import os
import re
import copy
import random
import numbers
import six
import datetime
import tensorflow as tf
print("Tensorflow version " + tf.__version__)
import pandas as pd
import pdb
import PIL
import numpy as np
from matplotlib import pyplot as plt
import matplotlib.collect... |
a61b60d48d5e8a931ee7ac6b9a157038993ac3162cc7f8a8b10b64262e7b88c2 | Python | 25,814 | 687 | from ...simulation import (
SimulatorAdapter,
SimulationComponent,
SimulationCell,
SimulationDevice,
TargetsNeurons,
TargetsSections,
SimulationResult,
SimulationRecorder,
)
from ...models import ConnectivitySet
from ...reporting import report, warn
from ...exceptions import *
from ...he... |
c9aa2e2fdaf0d325cfa2236945b46f6996f2fbb7f3d3515a42bc8beaf086e561 | Python | 25,832 | 591 | """ Module implementing GAN which will be trained using the Progressive growing
technique -> https://arxiv.org/abs/1710.10196
Code taken from -> https://github.com/akanimax/BMSG-GAN
"""
# import libraries and modules
import os
import sys
import time
import timeit
import torch.cuda
import torchvision.utils
fro... |
920b3f2f24bf6556c9274b50b5cfc998b4d6a9d5bfe57f2d5ee11d556c688bf6 | Python | 25,842 | 607 | # Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, so... |
856bbb664aa700d7e0366423ce803da6252659a8c3563075809c00572b5f9919 | Python | 25,855 | 718 | """
Compute the shortest paths and path lengths between nodes in the graph.
These algorithms work with undirected and directed graphs.
"""
import networkx as nx
__all__ = [
"shortest_path",
"all_shortest_paths",
"single_source_all_shortest_paths",
"all_pairs_all_shortest_paths",
"shortest_path_l... |
18ef8a79adeae011c4d773c655f4f751fef133100513e9e8b13ca90a097c5107 | Python | 25,898 | 527 | #!/usr/bin/env python3
import os
import numpy as np
import time
import torch
from torch import optim
# -custom-written libraries
from visual import visual_plt
import utils
from utils import checkattr
from param_stamp import get_param_stamp, get_param_stamp_from_args, visdom_name
from eval import evaluate, callbacks as ... |
b1a6fcc8d6a47e0a39734afe833995f11b34f0d30b9aa76d980ea7ba8d5e723d | Python | 25,901 | 507 | """Tests for sq.experimental.tl.make_stitched_labels."""
from __future__ import annotations
import numpy as np
import pytest
import squidpy as sq
def _qc_and_stitch(sdata, **stitch_kwargs):
sq.experimental.tl.calculate_tiling_qc(
sdata,
labels_key="labels",
tile_size=200,
nmads_... |
d7528ea51ed9bdc4e7277f97a9d9725246a3e386dd361edb1eb47889b5235bd6 | Python | 25,903 | 563 | """Graded, task-scoped gene-essentiality analysis (see issue #1076).
This replaces the earlier all-task binary scoring, which called a gene essential when
its knockout made *any* of the 57 tasks in ``metabolicTasks_Essential.txt`` infeasible
and compared that single boolean with the Hart 2015 fitness genes. The task l... |
91a638b291e5ad481e060775921cacb8c5a845b942d0d5933fa965a0f69a7eb0 | Python | 25,905 | 522 | # -*- coding: utf-8 -*-
import pandas as pd
import os
import copy
import numpy as np
import time
import re
from skimage import io
from scipy import ndimage
from scipy.ndimage import morphology
from matplotlib import pyplot as plt
input_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
... |
75d01844d73b333d408f59ca7fd209f94411df5afc954ccb8e4dca64b056a5ae | Python | 25,946 | 718 | import operator
from typing import Tuple
from ...datalog.expression_processing import conjunct_formulas
from nl_expr.expression_pattern_matching import add_match
from nl_expr.expression_walker import ExpressionWalker, PatternWalker
from nl_expr.expressions import (
Constant,
Definition,
FunctionApplication... |
8e55c3bc930c49644f316113d96640ce8ac5b16c152d43981bf1d51550e58332 | Python | 26,078 | 677 | """
Algorithm for testing d-separation in DAGs.
*d-separation* is a test for conditional independence in probability
distributions that can be factorized using DAGs. It is a purely
graphical test that uses the underlying graph and makes no reference
to the actual distribution parameters. See [1]_ for a formal
defini... |
6dd6fbab7d7491cf12b1918ffdbdf2cc372f49af9229d990eac5c37d9deaca3c | Python | 26,080 | 589 | """ Module implementing GAN which will be trained using the Progressive growing
technique -> https://arxiv.org/abs/1710.10196
Code taken from -> https://github.com/akanimax/BMSG-GAN
"""
# import libraries and modules
import os
import time
import timeit
import torchvision.utils
from tqdm import tqdm
import copy... |
84521456dfec6e2b07ecdf772b46fc82a0b843fbc37f2361f8fe626286a13fa6 | Python | 26,104 | 607 | #!/usr/bin/env python
# coding=utf-8
# Copyright 2020 The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LI... |
8b134287387d1f4ae608f42a2ce263fff986720221a2fdd5853676495ba5419a | Python | 26,105 | 668 | import threading
from typing import Any, Iterator, List, Mapping, Union
import anndata
import numpy as np
import pandas as pd
import torch
import torch.sparse
from scipy.sparse import spmatrix
class CellSampler():
"""An iterable cell dataset for minibatch sampling.
Attributes:
n_cells: number of cell... |
8d61005c639e737948a98f93477ee1da516a120077adff7fc963afa1fbe51252 | Python | 26,118 | 961 | import operator as op
import random
from itertools import product
from typing import AbstractSet, Callable, Tuple
from pytest import fixture, mark, raises, skip
from nl_expr import expression_walker as ew
from nl_expr import expressions
from ..basic_representation import DatalogProgram
from ..chase import (ChaseGener... |
aa0ae14e1c740ab5e114bfde9297c845fe8b4396d4704516285b52cb6136161b | Python | 26,145 | 567 | import os
os.environ["CUDA_DEVICE_ORDER"]="PCI_BUS_ID"
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
import numpy as np
import torch
from torch.autograd import Variable
from matplotlib import pyplot as plt
import pickle as pkl
from torch_geometric.data import Data, DataLoader
from tqdm import tqdm
import math
import random... |
5606e19031fda842ec346f561c4ab2ab300d740bc419fb4e824fa9066620764f | Python | 26,160 | 690 | """
General purpose plotting library
================================
.. module:: lib_plotting
:platform: Linux
:synopsis: module to easily-handle plotting functions
.. moduleauthor:: Jose M. Esnaola-Acebes <josemesnaola@gmail.com>
This library contains functions to format, modify and create figures, axes and ... |
b2082927cf20c4984db1b2aa7fba303423c9380d1a4c572c40f537eb14ea035b | Python | 26,205 | 737 | import math
import numpy as np
import pytest
import torch
from scipy.integrate import solve_ivp
from scipy.optimize import brentq
from spikingjelly.timing_based.neuron import Tempotron
def _ode_reference(times, indices, weights, duration, tau, tau_s, threshold):
"""Integrate physical current/voltage; do not use... |
f2c8583f8fe55914648f055a083ba1ae471906f602cc00a380542b8e2bc0523a | Python | 26,224 | 759 | """
Semantic similarity between documents and free-text queries.
Documents (for instance scientific articles identified by their PubMed
id) are embedded once with a SPECTER2 document adapter and cached on
disk. A free-text query is embedded with the SPECTER2 ad-hoc query
adapter and compared to every document by cosi... |
13f9e8859169aab1704ad5d599ecbe0b191569650e881f9b1ffcec1e59a33935 | Python | 26,245 | 658 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from unittest.mock import MagicMock, patch
import torch
from ax.adapter.factory import get_sobol
from... |
a1a62be34a42897ee0bef67696b24b8438aec2b38a2847587e0e497ee3d41129 | Python | 26,245 | 522 | # -*- coding: utf-8 -*-
import pandas as pd
import os
import copy
import numpy as np
import time
import re
from skimage import io
from scipy import ndimage
from scipy.ndimage import morphology
from matplotlib import pyplot as plt
input_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
... |
8fc58e9fcbe8140af5522ced752879a23162c10ffd2cc8d4ebaba7b7c065d29c | Python | 26,252 | 767 | from __future__ import annotations
from typing import Dict, Optional, Tuple
import numpy as np
import warnings
import numbers
import matplotlib.pyplot as plt
from abc import ABC, abstractmethod
from sklearn.neighbors import NearestNeighbors
from pynndescent import NNDescent
class YourCustomKNN(ABC):
... |
37acd526c33fbc3ad1fde9629a06dee1ed04d57a015b5f208190e0b38fc2af68 | Python | 26,263 | 686 | """Tests for the REPL driven from a web page."""
import json
from pathlib import Path
import pytest
pytest.importorskip("prompt_toolkit")
pytest.importorskip("rich")
import numpy as np # noqa: E402
from neurolang.frontend import NeurolangPDL # noqa: E402
from neurolang_apps.utils.tui import nifti # noqa: E402
f... |
3dac7dc593000070599d899e7bdc52e72daf27a8322d5f5ce9d161d67f4627b9 | Python | 26,304 | 617 | import pathlib
import shutil
from typing import Callable, Generator, Iterator, List
import pytest
from alpineer import test_utils
from ark.settings import EXAMPLE_DATASET_REVISION
from ark.utils.example_dataset import ExampleDataset, get_example_dataset
@pytest.fixture(scope="class", params=["segment_image_data",
... |
4067e600a00ddc6731e24a76f5133d45deb35d2c26be2b96093f1282e865420d | Python | 26,364 | 656 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from __future__ import annotations
from collections import defaultdict, OrderedDict
from collections.... |
79d9d2b542836416039786e9ed02aac8d7733dffce2d62211cdbb0e5df29a8bf | Python | 26,366 | 622 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from __future__ import annotations
import traceback
import warnings
from collections.abc import Itera... |
523a4188cd68f9d51800303212a09c6e5048b47823f2492b7821d760f5174cc2 | Python | 26,387 | 924 | # -*- coding: utf-8 -*-
"""
IO interface to read microscope and point data
This is the main module to distribute the reading and writing of individual data formats to the specialized sub-modules.
See :mod:`ClearMap.IO` for details.
"""
#:copyright: Copyright 2015 by Christoph Kirst, The Rockefeller University, New Y... |
94a639c5ce4d66dc01d6ca44f5750d33617b4148a277c3f3df10d345ebad9e29 | Python | 26,387 | 836 | """This file and its contents are licensed under the Apache License 2.0. Please see the included NOTICE for copyright information and LICENSE for a copy of the license."""
import logging
import os
import re
import shutil
import tempfile
from copy import deepcopy
from datetime import datetime, timedelta
from pathlib im... |
887266eaadef8be62de40ec0770acc2aa156ce0fedb31f22b4bd9f8845b2273e | Python | 26,397 | 638 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from copy import deepcopy
from math import isnan, nan
from typing import cast
import numpy as np
from... |
68773aa63e4b388e81e8d343f768a2a298b55124e913584185ecc2040636b716 | Python | 26,402 | 502 | import unittest as ut
from pysbm.sbm.model_selection import ModelSelectionByObjectiveFunctionValueOnly
from pysbm.sbm.model_selection import minimum_description_length_peixoto_first
from pysbm.sbm.model_selection import minimum_description_length_traditional
from pysbm.sbm.model_selection import minimum_description_len... |
08c447e29259b5383bf3312bf79364803dc177e58740239c43a1ed8df320f6ad | Python | 26,403 | 750 | # test_descriptive_report.py
# Contact: Jacob Schreiber <jmschreiber91@gmail.com>
import base64
import os
import shutil
import h5py
import numpy
import pytest
import modiscolite.descriptive_report
from modiscolite.descriptive_report import plot_to_base64
from modiscolite.descriptive_report import plot_histogram_to_... |
ec8dd3ec974d5b5e8dbbe866b0c5dc042c2504d4a5cf770961e6e353cfca0d70 | Python | 26,425 | 617 | """
Simulation of a bump attractor network for stimulus integration
===============================================================
.. module:: ring_simulation
:platform: Linux
:synopsis: simulation of the ring attractor network for stimulus integration tasks.
.. moduleauthor:: Jose M. Esnaola-Acebes <josemesna... |
88882680b55b5c150fa91286561d0394fd1a732cf7a9d8b0a5f43f3c08988489 | Python | 26,427 | 545 | """Scope gene-essentiality comparison to the reactions a model diff actually touches.
The global metrics in gene-essential_summary.md (allTaskMCC, growthAUROC, ...) are
computed over every gene Hart 2015 scored, so a pull request that edits a handful of
reactions is swamped by ftINIT's run-to-run non-determinism in th... |
341d6a0c5d7163391d7a5f5fa0e711a0676d356580ddf5f94e1e68bb251e5816 | Python | 26,449 | 615 | import logging
import os
from typing import (
Any,
Optional,
)
from rocrate.model.computationalworkflow import (
ComputationalWorkflow,
WorkflowDescription,
)
from rocrate.model.contextentity import ContextEntity
from rocrate.model.file import File
from rocrate.model.softwareapplication import Software... |
f3c094cf72fb4d099ddcb083be00a20eeaf4d5f5383e63ca3a9c0808b616c81d | Python | 26,452 | 622 | import numpy as np
from brian2.memory.dynamicarray import DynamicArray, DynamicArray1D
from brian2.core.variables import ArrayVariable, DynamicArrayVariable
from brian2.monitors.spikemonitor import SpikeMonitor
from brian2.monitors.statemonitor import StateMonitor
from brian2lava.utils.utils import DummyVariable
fro... |
19993e522206de2b225a91e11ed4ff422ca7ad0336986c0a68f0008aa4b5c84b | Python | 26,457 | 563 | # -*- coding:utf-8 -*-
import collections
import io
import math
import os.path
import tempfile
from collections import OrderedDict
from typing import List, Union
import keras
import tensorflow as tf
from keras import backend as K
from keras.api.layers import Dense, Concatenate, Flatten, Input, Add, BatchNormalization,... |
b4d78e0a3d31e5f9e13b75849aa4cec596b366eeeb06e00bd8755fd0a7d77ba9 | Python | 26,458 | 709 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import time
from collections.abc import Sequence
from logging import INFO, Logger
from ax.core.analys... |
f9e524a06ca3f835ce29fea0b6cf8fec14efb9ea7cc8c89db99a944bd8c00df5 | Python | 26,467 | 569 | """Materialise a stitched labels element from an assign_stitch_groups result.
Companion to :func:`squidpy.experimental.tl.assign_stitch_groups`. Takes the
piece-to-group mapping from ``stitch_group_id`` in the QC table and writes
a new labels element where stitched pieces share a single ID. The original
labels eleme... |
575cd327d322c908481f0e06157c56031b169165cc771a7ad49b14457cc37303 | Python | 26,492 | 894 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
cf4eab5f995819626243ba799daf268cbdf0294e1e33370a5f7830824e2f9343 | Python | 26,496 | 548 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
781c9cf6f207f0d67a8dfa3e2d89c8713111bebfb046bfb5eb4ddfc99faa3419 | Python | 26,498 | 623 | """Tests for batched motion energy computation.
Verifies that the batched implementation produces results equivalent
to the original per-filter implementation across backends and
batch sizes.
"""
import numpy as np
import pytest
import moten
from moten.backend import set_backend, get_backend
from moten import core
fr... |
b8a6274864fdf629d419179c8c56b0bdab1e55341836870fa0cd00a56c2b6be3 | Python | 26,550 | 929 | # -*- coding: utf-8 -*-
"""
IO interface to read microscope and point data
This is the main module to distribute the reading and writing of individual data formats to the specialized sub-modules.
See :mod:`ClearMap.IO` for details.
"""
#:copyright: Copyright 2015 by Christoph Kirst, The Rockefeller University, New Y... |
1d910d4819292968e84f1e5e08a63eae36da3ac37b22a66ecf79038ed4602d90 | Python | 26,580 | 807 | from __future__ import annotations
import shutil
from collections.abc import Mapping
from contextlib import ExitStack, contextmanager
from functools import singledispatch
from os import PathLike
from pathlib import Path
from typing import TYPE_CHECKING
import h5py
import numpy as np
import pandas as pd
import zarr
fr... |
64d447b99c9c25c39e83587cb6152cadfbc31e0bc3f35245dc69899ff977751d | Python | 26,582 | 804 | # test_affinitymat.py
# Contact: Jacob Schreiber <jmschreiber91@gmail.com>
import numpy
import scipy.sparse
import sklearn.preprocessing
import pytest
from modiscolite.affinitymat import _sparse_vv_dot
from modiscolite.affinitymat import cosine_similarity_from_seqlets
from modiscolite.affinitymat import jaccard_from_... |
2d8ef2f9f42eba0b1d24a0fe9336c2960af6392c0dde7ce280a0f3a453f4d2e9 | Python | 26,604 | 698 | """
Galaxy control queue and worker. This is used to handle 'app' control like
reloading the toolbox, etc., across multiple processes.
"""
import importlib
import json
import logging
import math
import socket
import sys
import threading
import time
from inspect import ismodule
from typing import (
Any,
cast,
... |
4394e71d90e4b731126eae32f45509b3dd42e94b3b3407ffc513caa3cce15510 | Python | 26,609 | 791 | from skimage import morphology, measure, io, util # For performing morphology operations (should maybe import more from skimage...)
from mpl_toolkits.mplot3d import Axes3D # Plotting in 3D
import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab import ... |
59af139b0fb22068eae0537715e6867b1c41c56168f37c180e45c925900a8cce | Python | 26,609 | 614 | # Copyright 2020 DeepMind Technologies Limited.
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agre... |
9a27d533f8e950aea3bfad176da8c1420ceba25fa7a6b0b4f97aa07d0ebd5a4e | Python | 26,613 | 676 | """Utility functions to retrieve measurements pertaining to cell density and stored in excel files
Measurements related to cell density are read and put under a uniform format so as to ease-off
computations made by their consumers of the densities module.
The two excel files to be handled are:
* mm3c.xls from the su... |
4bbc8ad10b880f118cb49550e583f384d4a934945f197c154304b9c13e51d4ba | Python | 26,662 | 766 | from __future__ import annotations
import argparse
import csv
import json
import os
import platform
import subprocess
import sys
import time
from pathlib import Path
from statistics import median
from typing import Any, Callable
import torch
try:
from benchmark.fp8_efficiency import (
assess_triton_effic... |
4ed3a05c341c25216d44f5298c970732010ddeb7d8f15e8411ef128afb77df1e | Python | 26,678 | 739 | """
Support for dynamically modifying output attributes.
"""
import logging
import re
from typing import (
Any,
List,
)
from typing_extensions import Protocol
from galaxy import util
from .util import resolve_tool_data_file
try:
from galaxy.util.template import fill_template
except ImportError:
fill... |
26c4130ffe772d809bbf597e74b2250efb7ec97b994ff5b357d1d6491ee12d19 | Python | 26,686 | 673 | import numpy as np
import pytest
import torch
from scipy.optimize import brentq
from spikingjelly.timing_based import functional, solver
from spikingjelly.timing_based.examples.cubic_srm_mnist import _CubicNet
def _linear(time, piece, start, slope):
return slope * (time - start) - 1, slope.expand_as(time)
@pyt... |
ec05bbac3a7f7ae72c0e8d6ff68343b32c630a58c278f6e6f86621e62ec2c048 | Python | 26,720 | 562 | from __future__ import annotations
import builtins
import logging
from typing import (
Optional,
TYPE_CHECKING,
TypedDict,
)
import jwt as pyjwt
from social_core.exceptions import (
AuthAlreadyAssociated,
AuthCanceled,
AuthForbidden,
AuthTokenError,
)
from social_core.utils import module_m... |
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